I do not understand why some of the flags that I raise, get eventually disputed although the question gets closed or why they do not appear at all in my flags counter. Specifically I have two questions when raising a flag in a question:
If I choose flag > it should be closed for another reason > ..., then I do not get this credited as a helpful flag (in the case of course that the question gets eventually closed). In fact it does not appear at all in my raised flags-counter. It is as if I did not raise the flag at all.
But if instead of choosing that, I choose flag > it is very low quality, then if the question gets closed for example because it is off-topic, my flag counts as disputed.
Since you have the 3K privilege, it actually is the case that you never raised the close-flag at all, because once you gain this privilege all "close-flags" are transformed into close votes.
A low-quality flag is disputed as soon as someone is the low quality review queue disagrees with your assessment, or even if the post is edited. This is because low quality flags are meant for posts which are unsalvagable. Not simply wrong, but so completely incoherent that there's no sense to them. An example would be: